G. Menschaert, X. Wang, AR. Jones, F. Ghali, D. Fenyö, et al. V. Olexiouk, B. Zhang, EW. Deutsch, T. Ternent, JA. Vizcaíno. (2018). The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. Genome Biology. 19(1),
JA. Vizcaíno, G. Mayer, SR. Perkins, H. Barsnes, M. Vaudel, et al. Y. Perez-Riverol, T. Ternent, J. Uszkoreit, M. Eisenacher, L. Fischer, J. Rappsilber, E. Netz, M. Walzer, O. Kohlbacher, A. Leitner, RJ. Chalkley, F. Ghali, S. Martínez-Bartolomé, EW. Deutsch, AR. Jones. (2017). The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & Cellular Proteomics. 16(7), pp.1275-1285.
F. Ghali, AR. Jones (2016). Proteogenomics: Proteomics for Genome Annotation. In: Proteome Informatics. The Royal Society of Chemistry, pp.365-384.
F. Ghali, R. Krishna, S. Perkins, A. Collins, D. Xia, et al. J. Wastling, AR. Jones. (2014). ProteoAnnotator – Open source proteogenomics annotation software supporting PSI standards. PROTEOMICS. 14(23-24), pp.2731-2741.
F. Ghali, R. Krishna, P. Lukasse, S. Martínez-Bartolomé, F. Reisinger, et al. H. Hermjakob, JA. Vizcaíno, AR. Jones. (2013). Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML. Molecular & Cellular Proteomics. 12(11), pp.3026-3035.
A. Cristea, F. Ghali, M. Joy (2011). Social, Personalized Lifelong Learning Personalized Lifelong Learning Personalized Lifelong Learning. IGI,
F. Ghali, AI. Cristea (2009). Social reference model for adaptive web learning. In: International Conference on Web-Based Learning. Springer Berlin Heidelberg, pp.162-171.
G. Menschaert, X. Wang, AR. Jones, F. Ghali, D. Fenyö, et al. V. Olexiouk, B. Zhang, EW. Deutsch, T. Ternent, JA. Vizcaíno. (2018). The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. Genome Biology. 19(1),
JA. Vizcaíno, G. Mayer, SR. Perkins, H. Barsnes, M. Vaudel, et al. Y. Perez-Riverol, T. Ternent, J. Uszkoreit, M. Eisenacher, L. Fischer, J. Rappsilber, E. Netz, M. Walzer, O. Kohlbacher, A. Leitner, RJ. Chalkley, F. Ghali, S. Martínez-Bartolomé, EW. Deutsch, AR. Jones. (2017). The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & Cellular Proteomics. 16(7), pp.1275-1285.
J. Fan, S. Saha, G. Barker, KJ. Heesom, F. Ghali, et al. AR. Jones, DA. Matthews, C. Bessant. (2015). Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics*. Molecular & Cellular Proteomics. 14(11), pp.3087-3093.
B. Wen, C. Du, G. Li, F. Ghali, AR. Jones, et al. L. Käll, S. Xu, R. Zhou, Z. Ren, Q. Feng, X. Xu, J. Wang. (2015). IPeak: An open source tool to combine results from multiple MS/MS search engines. PROTEOMICS. 15(17), pp.2916-2920.
R. Krishna, D. Xia, S. Sanderson, A. Shanmugasundram, S. Vermont, et al. A. Bernal, G. Daniel‐Naguib, F. Ghali, BP. Brunk, DS. Roos, JM. Wastling, AR. Jones. (2015). A large‐scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum. PROTEOMICS. 15(15), pp.2618-2628.
F. Ghali, R. Krishna, S. Perkins, A. Collins, D. Xia, et al. J. Wastling, AR. Jones. (2014). ProteoAnnotator – Open source proteogenomics annotation software supporting PSI standards. PROTEOMICS. 14(23-24), pp.2731-2741.
SL. Seymour, T. Farrah, P. Binz, RJ. Chalkley, JS. Cottrell, et al. BC. Searle, DL. Tabb, JA. Vizcaíno, G. Prieto, J. Uszkoreit, M. Eisenacher, S. Martínez‐Bartolomé, F. Ghali, AR. Jones. (2014). A standardized framing for reporting protein identifications in mzIdentML 1.2. PROTEOMICS. 14(21-22), pp.2389-2399.
J. Griss, AR. Jones, T. Sachsenberg, M. Walzer, L. Gatto, et al. J. Hartler, GG. Thallinger, RM. Salek, C. Steinbeck, N. Neuhauser, J. Cox, S. Neumann, J. Fan, F. Reisinger, Q-W. Xu, N. del Toro, Y. Pérez-Riverol, F. Ghali, N. Bandeira, I. Xenarios, O. Kohlbacher, JA. Vizcaíno, H. Hermjakob. (2014). The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience. Molecular & Cellular Proteomics. 13(10), pp.2765-2775.
F. Ghali, R. Krishna, P. Lukasse, S. Martínez-Bartolomé, F. Reisinger, et al. H. Hermjakob, JA. Vizcaíno, AR. Jones. (2013). Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML. Molecular & Cellular Proteomics. 12(11), pp.3026-3035.
JA. Medina‐Aunon, R. Krishna, F. Ghali, JP. Albar, AJ. Jones (2013). A guide for integration of proteomic data standards into laboratory workflows. PROTEOMICS. 13(3-4), pp.480-492.
F. Ghali, R. Krishna, P. Lukasse, S. Martinez-Bartolome, F. Reisinger, et al. H. Hermjakob, JA. Vizcaino, AR. Jones. (2013). A toolkit for the mzIdentML standard: the ProteoIDViewer, the mzidLibrary and the mzidValidator. Molecular & Cellular Proteomics. pp.mcp-O113.
D. Xia, F. Ghali, SJ. Gaskell, R. O'Cualain, PFG. Sims, et al. AR. Jones. (2012). Software for analysing ion mobility mass spectrometry data to improve peptide identification. PROTEOMICS. 12(12), pp.1912-1916.
F. Reisinger, R. Krishna, F. Ghali, D. Ríos, H. Hermjakob, et al. J. Antonio Vizcaíno, AR. Jones. (2012). jmz
S. Kluge, M. Hoffmann, D. Benndorf, E. Rapp, U. Reichl, et al. J. Merl, M. Ueffing, SM. Hauck, C. von Toerne, D. Xia, . others. (2012). Cell Biology. Proteomics. 12, pp.1893-2064.
AI. Cristea, F. Ghali (2011). Towards adaptation in e-learning 2.0. New Review of Hypermedia and Multimedia. 17(2), pp.199-238.
AI. Cristea, F. Ghali, M. Joy (2011). Social, personalized lifelong learning. E-infrastructures and technologies for lifelong learning: Next generation environments. pp.90-125.
F. Ghali, AR. Jones (2016). Proteogenomics: Proteomics for Genome Annotation. In: Proteome Informatics. The Royal Society of Chemistry, pp.365-384.
A. Cristea, F. Ghali, M. Joy (2011). Social, Personalized Lifelong Learning Personalized Lifelong Learning Personalized Lifelong Learning. IGI,
F. Ghali, AI. Cristea (2009). Social reference model for adaptive web learning. In: International Conference on Web-Based Learning. Springer Berlin Heidelberg, pp.162-171.
F. Ghali, AI. Cristea (2009). MOT 2.0: A Case Study on the Usefuleness of Social Modeling for Personalized E-Learning Systems. In: AIED. pp.333-340.
F. Ghali, AI. Cristea (2009). Authoring for e-learning 2.0: A case study. In: 2009 Ninth IEEE International Conference on Advanced Learning Technologies. IEEE, pp.170-174.
F. Ghali, AI. Cristea (2008). Evaluation of interoperability between MOT and regular learning management systems. In: European Conference on Technology Enhanced Learning. Springer Berlin Heidelberg, pp.104-109.
F. Ghali, AI. Cristea (2008). EVALUATION OF AUTHORING FOR ADAPTATION AND DELIVERY VIA LEARNING MANAGEMENT SYSTEMS. In: Proceedings of the 11th IASTED International Conference. pp.14-14.
F. Ghali, AI. Cristea, C. Stewart (2008). My online teacher 2.0.
F. Ghali, AI. Cristea (2008). Interoperability between MOT and learning management systems: converting CAF to IMS QTI and IMS CP. In: International Conference on Adaptive Hypermedia and Adaptive Web-Based Systems. Springer Berlin Heidelberg, pp.296-299.
F. Ghali, M. Sharp, AI. Cristea (2008). Folksonomies and ontologies in authoring of adaptive hypermedia. In: A3H: Sixth International Workshop on Authoring of Adaptive and Adaptable Hypermedia. pp.5-5.
T. Gross, F. Ghali, A. Cristea (2008). Communication and Collaboration Towards Problem Solving: Evaluation of PILS. In: 3rd European Conference on Technology Enhanced Learning EC-TEL 2008, IGACLE workshop. Maastricht, The Netherlands.
F. Ghali, AI. Cristea, C. Stewart, M. Hendrix (2008). Collaborative adaptation authoring and social annotation in MOT. In: A3H: Sixth International Workshop on Authoring of Adaptive and Adaptable Hypermedia. pp.54-54.
F. Ghali, J. Foss User Guide on the Concept Adaptation Model Tool. University of Warwick
T. Ternent, F. Ghali, D. Fenyo, AR. Jones, JA. Vizcaíno (2016). proBed: extension of the BED format for mapping peptides identified by mass spectrometry to a genome.